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PlantCV v3.13.0
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@HaleySchuhl HaleySchuhl released this 29 Jul 21:25
v3.13.0
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PlantCV Version 3.13 Updates

  • Update imports to discontinue the deprecation warnings in pcv.watershed
  • Update scikit-image requirement to scikit-image>=0.13
  • Reorganizes our tutorials in several ways:
    • There is now a main tutorials page that is organized as a gallery of tutorial "cards" that can be filtered by keyword tags. Each card has a launch Binder button to access the interactive tutorial and a link to the static tutorial.
    • The tutorial card images and links to notebooks are remote and can be hosted from any GitHub (or other) repository.
    • The static tutorial pages are now grouped in a directory called "tutorials."
    • The static tutorial pages now only have a launch Binder button and render the complete Jupyter notebooks using nbviewer, rather than having a page that recreates the workflow and has a script version of the workflow.
  • Added pcv.transform.gamma_correct which performs gamma correction on the input image (wrapper of the skimage gamma correction function).
  • Updated the debug method in the backend within more miscellaneous functions.
  • Expand the functionality of the metadata matcher portion of plantcv-workflow to support the matching of multiple metadata values.
    • Syntax at the command line (--match id:1,id:2,id:3)
    • Also supports lists in configuration file based parallelization
  • Updates plantcv.hyperspectral.read_data to support Band Sequential (BSQ) in addition to Band Interleaved by Line (BIL) raw data formats for ENVI type multi/hyperspectral datasets.
  • Adds pcv.visualize.obj_sizes function for annotating the sizes of separate objects onto a visualization.
  • Add pcv.visualize. obj_size_ecdf for a new way to visualize: empirical cumulative distribution function (eCDF).
  • Converted to base python classes int and bool since numpy is deprecating np.int and np.bool datatypes.
  • Update the fill_segments function in the morphology sub-package
    • The added observations are corrected.
    • Also return the filled_mask (which is a label image as an output) along with the filled_image as outputs.
    • The filled_img is generate by calling the added colorize_label_img visualization function.
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